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News

Phylosymbiosis in Fish Microbiota

Despite the rapid diversification of morphology and behaviors among pupfish species, gut microbiota related much more closely to the phylogenies of their hosts than to their life history. Reported by the Martin lab (Integrative Biology) in PLOS ONE, September 16, 2022.

Photograph of a pupfish (Cyprinodon sp.), Wikimedia Commons.

Probing Contaminated Environments

From the Terry group (Plant and Microbial Biology): Description of culture-dependent and culture-independent bacterial diversity in contaminated wastewater. Published in Journal of Environmental Management.

Nutrient Profiles Across Microbiomes

Cobamides are important nutrients in microbial communities that can act as public goods, so cobamide availability in a habitat might shape the structure of microbial interactions. New research from the Taga lab characterizes variation in cobamide composition across insect and mammalian guts and environmental samples. Published August 29, 2022 in Biochemistry.

From Hallberg et al. 2022, Biochemistry.

Bouncing Back After Drought

A new study from the Taylor lab reports that soil fungi are generally more drought-resistant than bacteria, but also that drought disrupts intra- and inter-kingdom correlations in microbial co-occurrence networks. Published July 5, 2022 in Nature Communications.

Microbiome Method Development

Berkeley scientists contributed to two books this summer on characterizing the structure and importance of microbial communities. Learn how to properly run a microbiome GWAS in Methods in Molecular Biology, or read about soil microbiology in desert ecosystems in Microbiology of Hot Deserts. Congratulations to the Coleman-Derr and Northen groups!

From Van Goethem et al. 2022, Microbiology of Hot Deserts pp. 37-63.

Rewriting the Genetic Code

New work from the Banfield lab finds alternative stop codons are widely distributed among phage genomes, including in phages of human and animal gut microbiota. Stop codon has appeared repeatedly in closely related lineages, suggesting it can evolve rapidly. Published May 26, 2022 in Nature Microbiology.

Natural Product Discovery

New paper from the Traxler lab describes the discovery of a new family of antimicrobial compounds, referred to as the dynaplanins. The approach took advantage of natural patterns of antimicrobial production and resistance among soil actinomycetes. Published May 24, 2022 in mBio and selected as a 2022 Editor’s Pick.

Analyzing Adaptability

The Chakraborty lab describes how strains within the genus Arthrobacter have adapted to a variety below-ground environments. Published March 30, 2022 in ISME Communications: https://doi.org/10.1038/s43705-022-00113-8

Core Taxa Respond to Fertilizer

The Koskella Lab describes how fertilizer alters the tomato rhizosphere microbiome. Published March 21, 2022 in Applied and Environmental Microbiology: https://doi.org/10.1128/aem.00049-22

The Rarefaction Debate

New work from the Fithian group reports a rarefaction efficiency index to determine the sensitivity of microbiome data to loss upon rarefaction and guide the decisions of researchers. Published February 25, 2022 in Bioinformatics: https://doi.org/10.1093/bioinformatics/btac127.

Single-Cell Sequencing Provides New Insights

The Joint Genome Institute demonstrates how single-cell sequencing reveals population structure in the microbial communities of hot springs. Published December 30, 2021 in ISME: https://doi.org/10.1093/femsec/fiab162.

Sequencing Salamanders

The Rosenblum lab reports host and habitat influences on the microbial communities living on salamanders. Published December 16, 2021 in FEMS Microbiology Ecology: https://doi.org/10.1093/femsec/fiab162

Genome Editing in Communities

The Banfield and Doudna labs announce DART-ET-seq, a method for targeted DNA insertion in a community context. Published December 6, 2021 in Nature Microbiology: https://doi.org/10.1038/s41564-021-01014-7.

New Data Sharing Initiative

Announcement of the National Microbiome Data Collaborative Data Portal, a resource for hosting microbiome data that is accessible and usable across systems and studies: https://academic.oup.com/nar/article/50/D1/D828/6414581

Predicting Persistence

New work from the Banfield Lab (Environmental Science, Policy, and Management) identifies traits of bacteria that help them to survive the infant gut. Published September 21st, 2021 in Cell Reports Medicine: https://doi.org/10.1016/j.xcrm.2021.100393

Better Together: CRAGE + CRISPR

The Yoshikuni group (Lawrence Berkeley Lab) integrates chassis-independent recombinase-assisted genome engineering with CRISPR to rapidly profile the function of bacterial biosynthetic gene clusters. Published September 10th, 2021 in Cell Chemical Biology: https://doi.org/10.1016/j.chembiol.2021.08.009

Microbial Arms Races

A multi-year study from the Koskella lab (Integrative Biology) describes co-evolutionary arms races between bacteria and phages in natural microbial communities. Published in The American Naturalist:  https://doi.org/10.1086/717181

Fungi Around the World

A new study from the Dawson lab (Integrative Biology) analyzes biogeographic patterns of free-living and host-associated fungi. Read more in Ecology Letters: https://doi.org/10.1111/ele.13886

Adding Branches to the Tree of Life

Congratulations to the Banfield Lab (Environmental Science, Policy, and Management) for two new publications describing the diversity and metabolic capabilities of the largely uncultivated, ultra-small bacteria comprising the Candidate Phyla Radiation. Published July 13th, 2021 and August 17th, 2021 in mSystems: https://doi.org/10.1128/mBio.00521-21, https://doi.org/10.1128/mSystems.01205-20

Expanding Phage Collections

Nikos Kyrpides (Joint Genome Institute) and colleagues compiled a database of nearly 200,000 bacteriophage genomes and predicted protein clusters. Published June 24, 2021 in Nature Microbiology: https://doi.org/10.1038/s41564-021-00928-6

Iron Metabolism in Drought

Drought stress disrupts iron homeostasis in plant roots, leading to changes in root-associated microbial communities. Published by the Coleman-Derr lab (Plant and Microbial Biology) in Nature Communications, May 28, 2021: https://doi.org/10.1038/s41467-021-23553-7

Protists in the Microbiome

A large-scale field experiment from the Firestone lab (Environmental Science, Policy, and Management) shows that distinct protist communities inhabit the rhizosphere in different plant developmental stages, shedding new light on an understudied component of the plant microbiome. Published April 28, 2021 in Microbiome: https://doi.org/10.1186/s40168-021-01042-9

New Single-Cell Sequencing Pipeline

New pipeline developed by Jan-Feng Cheng (Joint Genome Institute) and colleagues for single-cell sequencing of microbial eukaryotes. Published April 23, 2021 in iScience: https://www.cell.com/iscience/pdf/S2589-0042(21)00258-3.pdf

Ploidy Problems

New work from the Coleman-Derr lab (Plant and Microbial Biology) evaluated the contributions of polyploidy and domestication to wheat microbiome composition. Published March 18, 2021 in PLOS One: https://doi.org/10.1371/journal.pone.0248030

Biofilms in Oral Bacteria

The Zhang lab (Chemical and Biomolecular Engineering) identified biochemical mechanisms of adhesion and biofilm formations in Streptococcus mutans, a significant contributor to tooth decay in the human oral microbiota. Published March 4, 2021 in Nature Chemical Biology: https://doi.org/10.1038/s41589-021-00745-2

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